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Reference SNP (refSNP) Cluster Report: rs6874642                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.1338/670 (1000 Genomes)
T=0.1503/18875 (TOPMED)
HGVS Names
  • CM000667.2:g.150112733C>T
  • NC_000005.10:g.150112733C>T
  • NC_000005.9:g.149492296C>T
  • NG_012303.1:g.5640G>A
  • NG_023367.1:g.48127G>A
  • NM_005211.3:c.-181+528G>A
Links , Linkout
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss278528542 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6874642 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss10220330BCM_SSAHASNP|chr5.NT_029289.9_10655233byFreqfwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc06/27/0310/25/06116Genomicunknown
ss24684972PERLEGEN|afd3328094byFreqfwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc08/10/0409/13/04123Genomicunknown
ss67511001ILLUMINA|HumanHap550v1.1_rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc11/14/0611/14/06127Genomicunknown
ss67874853ILLUMINA|HumanHap650Yv1.0_rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc11/14/0611/14/06127Genomicunknown
ss68262411ILLUMINA|HumanHap250Sv1.0_rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc12/06/0612/07/06127Genomicunknown
ss68953553PERLEGEN|PGP03328094byFreqfwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc01/30/0703/31/08127Genomicunknown
ss70892882ILLUMINA|HumanHap550v3.0__rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc04/20/0703/31/08130Genomicunknown
ss71486262ILLUMINA|HumanHap650Yv3.0_rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc04/23/0704/23/07127Genomicunknown
ss75577872ILLUMINA|ILMN_Human_1M_rs6874642fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc08/28/0708/29/07129Genomicunknown
ss84566704KRIBB_YJKIM|KHS745624fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc12/04/0712/07/07130Genomicunknown
ss93288955BCMHGSC_JDW|JWB-2055419byFreqfwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc02/26/0809/05/14129Genomicunknown
ss143525182ENSEMBL|ENSSNP12937246fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc06/05/0906/06/09131Genomicunknown
ss154389133ILLUMINA|Human610_Quadv1_B_rs6874642-128_B_F_1502247177fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc06/18/0906/20/09131Genomicunknown
ss159564817ILLUMINA|Human660W-Quad_v1_A_rs6874642-128_B_F_1502247177fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc07/06/0907/07/09131Genomicunknown
ss167221073COMPLETE_GENOMICS|NA20431_36_chr5_149472489fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc09/30/0909/30/09132Genomicunknown
ss174149954ILLUMINA|Human1M-Duov3_B_rs6874642-128_B_F_1502247177fwd/BC/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc10/01/0910/04/09132Genomicunknown
ss2331959811000GENOMES|pilot_1_CEU_2800610_chr5_149472489fwd/C/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc05/01/1005/01/10132Genomicunknown
ss2403091651000GENOMES|pilot_1_CHB+JPT_2194242_chr5_149472489fwd/C/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc05/01/1005/01/10132Genomicunknown
ss278528542GMI|GMI_AK_SNP_2848781fwd/C/Tgggctttgtatggccaggccttatagccgtgggtattttccctggtgtggctcagctgcc12/16/1012/16/10137Genomicunknown
ss483894344ILLUMINA|HumanOmni2.5-4v1_D_kgp7358304-0_B_F_1823205803fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag01/30/1210/28/16137Genomicunknown
ss484959824ILLUMINA|HumanOmni2.5-4v1_B_SNP5-149472489-0_B_F_1619187925fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag01/30/1210/28/16137Genomicunknown
ss536089059ILLUMINA|HumanOmni5-4v1_B_kgp7358304-0_B_F_1823205803fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag06/22/1208/29/15146Genomicunknown
ss558791397TISHKOFF|snp_chr5_149492296fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag11/22/1211/23/12138Genomicunknown
ss652695297SSMP|5_149492296fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag12/14/1202/11/15138Genomicunknown
ss780448402ILLUMINA|HumanOmni25Exome-8v1_A_kgp7358304-0_B_F_1823205803fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag05/30/1307/09/15146Genomicunknown
ss782390806ILLUMINA|HumanOmni2.5-4v1_H_kgp7358304-0_B_F_1823205803fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag05/30/1307/28/15146Genomicunknown
ss835938258ILLUMINA|HumanOmni2.5-8v1_A_kgp7358304-0_B_F_1823205803fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag09/18/1307/28/15146Genomicunknown
ss982253789EVA-GONL|EVA-GONL_rs6874642fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag04/23/1404/24/14142Genomicunknown
ss1073137410JMKIDD_LAB|HGDP_WGS_chr5_149492296fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag07/10/1407/11/14142Genomicunknown
ss13177294981000GENOMES|PHASE3_V1_29579783fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag08/16/1408/16/14142Genomicunknown
ss1430538327DDI|DDI_rs6874642fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag11/04/1411/05/14144Genomicunknown
ss1581399951EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6874642fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag02/19/1502/20/15144Genomicunknown
ss1591786566EVA_DECODE|EVA_DECODE_5_149472489_1117271_rs6874642fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag03/02/1503/03/15144Genomicunknown
ss1614287884EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_149492296_16373370fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag03/04/1503/04/15144Genomicunknown
ss1657281917EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_149492296_16373370fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag03/04/1503/04/15144Genomicunknown
ss1712809984EVA_SVP|EVA_SVP_504351fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag03/12/1503/12/15144Genomicunknown
ss1925507725WEILL_CORNELL_DGM|SNV:chr5:149492296fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag10/16/1510/17/15147Genomicunknown
ss1970236834GENOMED|rs6874642fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag02/16/1602/16/16147Genomicunknown
ss2023361685JJLAB|SNP3864240fwd/BC/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag08/29/1608/30/16149Genomicunknown
ss2151520220USC_VALOUEV|NC_000005.9:g.149492296C>Tfwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag11/17/1611/17/16150Genomicunknown
ss2279231998HUMAN_LONGEVITY|HLI-5-150112733-C-Tfwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag11/18/1611/18/16150Genomicunknown
ss2447550830TOPMED|5_149492296_C/Tfwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag11/20/1611/20/16150Genomicunknown
ss2626169432SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2473349fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag01/06/1701/06/17151Genomicunknown
ss2634356051ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp7358304-0_B_F_182320580fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag02/02/1702/02/17151Genomicunknown
ss2634356052ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs6874642-131_B_F_18897791fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag02/02/1702/02/17151Genomicunknown
ss2707089947GRF|rs6874642fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag02/13/1702/13/17151Genomicunknown
ss2832248522GNOMAD|rs6874642fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag05/18/1705/18/17151Genomicunknown
ss2997996975SWEGEN|NC_000005.9:g.149492296C>Tfwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag05/30/1705/30/17151Genomicunknown
ss3025462668BIOINF_KMB_FNS_UNIBA|5.150112733C>Tfwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag07/05/1707/05/17151Genomicunknown
ss3346682725CSHL|rs6874642fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag10/02/1710/02/17151Genomicunknown
ss3482057616TOPMED|TOPMed_freeze_5?chr5:150,112,733fwd/C/Tttgtatggccaggccttatagccgtgggtattttccctggtgtggctcag10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6874642|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 AAACAAAAAC AAACAAAACA ACAACAGCTT GGACTGGTGT CTCATCTGTA ACATGGGATA
 ATAGTAGGAC TCAGGTCACT GGGCTTTTGG GAGGGTAAAA TGAGCTAATG TGTGTGAAGC
 AACCAGACAG CCCTGGGGCA TAGTAACTGT TGGATAGTGG TAGTCAGATT TTTATCAACC
 TTTGTCTTAG TGTGGCATCT AGCTCCATTT ATCCCTGGGG AAACTGAGGC CTGATGTGGT
 GTAATCCACT CAAGTTCCCA TAAGGAGCAG GCCTGAGACA CAGGGAGCTG AGATCTTCTG
 ACCTCCAGAC AGAGGCTTTT GCACCAGCAA AGATAATCCC TGTCTGGAAT GTGGGCTAGT
 TATTTTCTTT ACAAGGCAGA TCCGGGTATC ACCTCATTCA ACTCCTGCCA CAGCTAGAAG
 AGAAGTCACA GGCTCTGGGT GTTTTCTGAA GCCAGGATCC CTGGGATGGT GGGCTTTGTA
 TGGCCAGGCC TTATAGCCGT
 Y
 GGGTATTTTC CCTGGTGTGG CTCAGCTGCC CCTGAGTTGG CGGCTGGGCC TGTGAGTCAG
 AGCTGTCCCA TGGCTCCATT CTTTTCCCCA CTTGAAGCCA CAGCCCCAGA CTCCTGGAGG
 CAGTCCAGGG AGGCCTGTGG TTCCAAAATG AGGTCCTTCC CGCACCCACT CAAATGAAGA
 TGCCGTTTCC CCAGCTCAGA GAGAGCAAGG GAGGGGCTAA GGACACACAG TGATGGATCT
 GAGGCTGACA TCTGGTCCAC CTCAAGTGAG CCAAGTACAG GACTCTGGGC CCAGGTGGGA
 GGGCCCTAGC ACTCTGTCCC CTGCCCCCAG CAACCCTATT GCCCCTGGCC CTGTGTTGCT
 GCCGGGGTCC CACAGGCCTG GGCTCGGCAG GAGAGCCTAT GACTCATGCC GGCCCCACAA
 CCCCTGAGAT GCTGCAGCCG TGAGGGGTCT GGGTCCTGCC AGGTCTACAC CTCTCTGCCC
 TCAAAGCCAC AGCCTGGTCG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029289
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC
C/C
C/T
T
T/T
HWPC
T
ss10220330CHMJAsian 74IG0.95945948 0.04054054 0.959459480.04054054
ss1317729498EAS 1008AF 0.911700010.08830000
EUR 1006AF 0.794200000.20580001
AFR 1322AF 0.994700010.00530000
AMR 694AF 0.703200040.29680002
SAS 978AF 0.835399990.16460000
ss143525182ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss167221073PGP 2IG 1.00000000 0.500000000.50000000
ss233195981pilot_1_CEU_low_coverage_panel 120AF 0.841666640.15833333
ss240309165pilot_1_CHB+JPT_low_coverage_panel 120AF 0.975000020.02500000
ss24684972AFD_EUR_PANELEuropean 48IG 0.500000000.50000000 0.294266000.750000000.25000000
AFD_AFR_PANELAfrican American 46IG 0.869565190.13043478 1.000000000.934782620.06521739
AFD_CHN_PANELAsian 48IG 0.916666690.08333334 1.000000000.958333310.04166667
ss68953553HapMap-CEUEuropean 120IG 0.666666690.31666666 0.016666670.479500000.824999990.17500000
HapMap-HCBAsian 90IG 0.822222230.15555556 0.022222220.371093000.899999980.10000000
HapMap-JPTAsian 90IG 0.911111120.08888889 1.000000000.955555560.04444445
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss93288955HapMap-CEUEuropean 226IG 0.681415920.29203540 0.026548671.000000000.827433650.17256637
HapMap-HCBAsian 86IG 0.813953460.16279070 0.023255810.402784000.895348850.10465116
HapMap-JPTAsian 172IG 0.906976760.08139535 0.011627910.099721000.947674390.05232558
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.918367330.08163265 1.000000000.959183690.04081633
HAPMAP-CHBAsian 82IG 0.926829280.07317073 1.000000000.963414610.03658536
HAPMAP-CHD 168IG 0.857142870.13095239 0.011904760.479500000.922619040.07738096
HAPMAP-GIH 176IG 0.784090940.17045455 0.045454550.020022000.869318190.13068181
HAPMAP-LWK 180IG 0.977777780.02222222 1.000000000.988888860.01111111
HAPMAP-MEX 100IG 0.560000000.28000000 0.160000000.020022000.699999990.30000001
HAPMAP-MKK 286IG 0.867132840.12587413 0.006993010.751830000.930069920.06993007
HAPMAP-TSI 176IG 0.647727250.31818181 0.034090911.000000000.806818190.19318181
ENSEMBL_Watson 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.232+/-0.2490000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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